BDD Tests for py-ard

BDD Tests for py-ard

Author: rsajulga-nmdp

.gitignore

@@ -104,3 +104,7 @@ ENV/
 *.txt 
 *.pickle
 *.zip
+
+# BDD Testing
+testing/
+!test-requirements.txt

README.rst

@@ -34,6 +34,21 @@ Install from PyPi
 
     pip install py-ard
 
+Testing
+
+-------
+To run behavior-driven development (BDD) tests locally via the behave framework, 
+you'll need to set up a virtual environment.
+
+.. code-block::
+    # Virtual environment setup
+    python3 -m venv testing
+    source testing/bin/activate
+    pip install --upgrade pip
+    pip install -r test-requirements.txt
+
+    # Running Behave and all BDD tests
+    behave
 
 Example
 -------

behave.ini

@@ -0,0 +1,7 @@
+[behave]
+paths=tests
+format=pretty
+show_snippets=false
+
+; Development
+stop=true

test-requirements.txt

@@ -0,0 +1,3 @@
+behave==1.2.6
+pandas==0.25.1
+PyHamcrest==2.0.2

tests/environment.py

@@ -0,0 +1,4 @@
+from pyard import ARD
+
+def before_all(context):
+    context.ard = ARD(verbose=True)

tests/features/allele.feature

@@ -0,0 +1,23 @@
+Feature: Alleles
+
+        Scenario Outline:
+
+                Given the allele as <Allele>
+                When reducing on the <Level> level
+                Then the reduced allele is found to be <Redux Allele>
+
+                Examples:
+                        | Allele         | Level | Redux Allele    |
+                        | A*01:01:01     | G     | A*01:01:01G     | 
+                        | A*01:01:01     | lg    | A*01:01g        |
+                        | A*01:01:01     | lgx   | A*01:01         |
+
+                        | HLA-A*01:01:01 | G     | HLA-A*01:01:01G |
+                        | HLA-A*01:01:01 | lg    | HLA-A*01:01g    |
+                        | HLA-A*01:01:01 | lgx   | HLA-A*01:01     |
+
+                        | DRB1*14:05:01  | lgx   | DRB1*14:05      |
+                        | DRB1*14:05:01  | lg    | DRB1*14:05g     |
+                        
+                        | DRB1*14:06:01  | lgx   | DRB1*14:06      |
+                        | DRB1*14:06:01  | lg    | DRB1*14:06g      |

tests/features/glstring.feature

@@ -0,0 +1,21 @@
+Feature: GL (Genotype List) Strings
+
+        Scenario Outline:
+
+                Given the allele as <Allele>
+                When reducing on the <Level> level (ambiguous)
+                Then the reduced allele is found to be <Redux Allele>
+
+                Examples:
+                        | Allele      | Level | Redux Allele                |
+                        | A*01:01:01:01+A*01:01:01:01         | G   | A*01:01:01G+A*01:01:01G |
+                        | HLA-A*01:01:01:01+HLA-A*01:01:01:01 | G   | HLA-A*01:01:01G+HLA-A*01:01:01G |
+                        | A*01:01:01:01+A*01:01:01:01         | lg  | A*01:01g+A*01:01g |
+                        | HLA-A*01:01:01:01+HLA-A*01:01:01:01 | lg  | HLA-A*01:01g+HLA-A*01:01g |
+                        | A*01:01:01:01+A*01:01:01:01         | lgx | A*01:01+A*01:01 |
+                        | HLA-A*01:01:01:01+HLA-A*01:01:01:01 | lgx | HLA-A*01:01+HLA-A*01:01 |
+                        | A*01:01+A*01:01^B*07:02+B*07:02     | G   | A*01:01:01G+A*01:01:01G^B*07:02:01G+B*07:02:01G |
+                        | A*01:01+A*01:01^B*07:02+B*07:02     | lg  | A*01:01g+A*01:01g^B*07:02g+B*07:02g |
+                        | A*01:01~B*07:02+A*01:01~B*07:02     | G   | A*01:01:01G~B*07:02:01G+A*01:01:01G~B*07:02:01G |
+                        | A*01:01~B*07:02+A*01:01~B*07:02     | lg  | A*01:01g~B*07:02g+A*01:01g~B*07:02g |
+                        | A*01:01~B*07:02+A*01:01~B*07:02\|A*02:01~B*07:02+A*02:01~B*07:02 | lg | A*01:01g~B*07:02g+A*01:01g~B*07:02g\|A*02:01g~B*07:02g+A*02:01g~B*07:02g |

tests/features/mac.feature

@@ -0,0 +1,14 @@
+Feature: MAC (Multiple Allele Code)
+
+        Scenario Outline:
+
+                Given the allele as <Allele>
+                When reducing on the <Level> level (ambiguous)
+                Then the reduced allele is found to be <Redux Allele>
+
+                Examples:
+                        | Allele      | Level | Redux Allele                |
+                        | A*01:AB     | G     | A*01:01:01G/A*01:02         |
+                        | A*01:AB     | lgx   | A*01:01/A*01:02             | 
+                        | HLA-A*01:AB | G     | HLA-A*01:01:01G/HLA-A*01:02 | 
+                        | HLA-A*01:AB | lgx   | HLA-A*01:01/HLA-A*01:02     | 

tests/features/p_g_group.feature

@@ -0,0 +1,12 @@
+Feature: P and G Groups
+
+        Scenario Outline:
+
+                Given the allele as <Allele>
+                When reducing on the <Level> level (ambiguous)
+                Then the reduced allele is found to be <Redux Allele>
+
+                Examples:
+                        | Allele      | Level | Redux Allele                |
+                        | A*02:01P    | lgx   | A*02:01                     |
+                        | A*02:01:01G | lgx   | A*02:01                     |

tests/steps/redux_allele.py

@@ -0,0 +1,19 @@
+from hamcrest import assert_that, is_
+
+@given('the allele as {allele}')
+def step_impl(context, allele):
+    context.allele = allele
+
+@when('reducing on the {level} level')
+def step_impl(context, level):
+    context.level = level
+    context.redux_allele = context.ard.redux(context.allele, level)
+
+@when('reducing on the {level} level (ambiguous)')
+def step_impl(context, level):
+    context.level = level
+    context.redux_allele = context.ard.redux_gl(context.allele, level)
+
+@then('the reduced allele is found to be {redux_allele}')
+def step_impl(context, redux_allele):
+    assert_that(context.redux_allele, is_(redux_allele))